BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 011172
(492 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme
Length = 883
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 72/327 (22%), Positives = 120/327 (36%), Gaps = 82/327 (25%)
Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189
L R Q+ +E E++E ++ + +AD K + LP + + WFE
Sbjct: 32 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 91
Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249
++ + K T + + + +A IT+ + L T+A V A
Sbjct: 92 VK----------AKRGKRPTAFQFLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 140
Query: 250 IGEAIENEA---RIQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306
IG AIE+EA RI+ KKN + RV +
Sbjct: 141 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 178
Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQ----L 356
KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q +
Sbjct: 179 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVV 237
Query: 357 GDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPL 416
G I L EA+ R + P+ + P +VPP
Sbjct: 238 GQDSETIE------LAPEYAEAIATRAGALAGISPM---------------FQPCVVPPK 276
Query: 417 NWRGYNRGGHFF---LPSYVMRTHGAR 440
W G GG++ P ++RTH +
Sbjct: 277 PWTGITGGGYWANGRRPLALVRTHSKK 303
>pdb|2PI4|A Chain A, T7rnap Complexed With A Phi10 Protein And Initiating Gtps.
pdb|2PI5|A Chain A, T7 Rna Polymerase Complexed With A Phi10 Promoter
Length = 878
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 72/327 (22%), Positives = 119/327 (36%), Gaps = 82/327 (25%)
Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189
L R Q+ +E E++E ++ + +AD K + LP + + WFE
Sbjct: 27 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 86
Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249
++ K Q + + + +A IT+ + L T+A V A
Sbjct: 87 VKAKRGKRPTAFQ----------FLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 135
Query: 250 IGEAIENEA---RIQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306
IG AIE+EA RI+ KKN + RV +
Sbjct: 136 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 173
Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQ----L 356
KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q +
Sbjct: 174 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVV 232
Query: 357 GDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPL 416
G I L EA+ R + P+ + P +VPP
Sbjct: 233 GQDSETIE------LAPEYAEAIATRAGALAGISPM---------------FQPCVVPPK 271
Query: 417 NWRGYNRGGHFF---LPSYVMRTHGAR 440
W G GG++ P ++RTH +
Sbjct: 272 PWTGITGGGYWANGRRPLALVRTHSKK 298
>pdb|4RNP|A Chain A, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|B Chain B, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|C Chain C, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|1CEZ|A Chain A, Crystal Structure Of A T7 Rna Polymerase-T7 Promoter
Complex
pdb|1QLN|A Chain A, Structure Of A Transcribing T7 Rna Polymerase Initiation
Complex
pdb|1H38|A Chain A, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|B Chain B, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|C Chain C, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|D Chain D, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1MSW|D Chain D, Structural Basis For The Transition From Initiation To
Elongation Transcription In T7 Rna Polymerase
pdb|1S0V|A Chain A, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|B Chain B, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|C Chain C, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|D Chain D, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S76|D Chain D, T7 Rna Polymerase Alpha Beta Methylene Atp Elongation
Complex
pdb|1S77|D Chain D, T7 Rnap Product Pyrophosphate Elongation Complex
Length = 883
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 72/327 (22%), Positives = 120/327 (36%), Gaps = 82/327 (25%)
Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189
L R Q+ +E E++E ++ + +AD K + LP + + WFE
Sbjct: 32 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 91
Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249
++ + K T + + + +A IT+ + L T+A V A
Sbjct: 92 VK----------AKRGKRPTAFQFLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 140
Query: 250 IGEAIENEA---RIQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306
IG AIE+EA RI+ KKN + RV +
Sbjct: 141 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 178
Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQ----L 356
KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q +
Sbjct: 179 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVV 237
Query: 357 GDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPL 416
G I L EA+ R + P+ + P +VPP
Sbjct: 238 GQDSETIE------LAPEYAEAIATRAGALAGISPM---------------FQPCVVPPK 276
Query: 417 NWRGYNRGGHFF---LPSYVMRTHGAR 440
W G GG++ P ++RTH +
Sbjct: 277 PWTGITGGGYWANGRRPLALVRTHSKK 303
>pdb|3E2E|A Chain A, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 7nt Of Rna
pdb|3E3J|C Chain C, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 8nt Of Rna
pdb|3E3J|B Chain B, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 8nt Of Rna
Length = 889
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 72/326 (22%), Positives = 120/326 (36%), Gaps = 80/326 (24%)
Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189
L R Q+ +E E++E ++ + +AD K + LP + + WFE
Sbjct: 38 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 97
Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249
++ + K T + + + +A IT+ + L T+A V A
Sbjct: 98 VK----------AKRGKRPTAFQFLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 146
Query: 250 IGEAIENEA---RIQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306
IG AIE+EA RI+ KKN + RV +
Sbjct: 147 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 184
Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSP 360
KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q
Sbjct: 185 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQ----- 238
Query: 361 PDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLE-KTGRHMIIPYM--PMLVPPLN 417
+ G+ IE P + + + G I M P +VPP
Sbjct: 239 ---------------NAGVVGQDSETIELAPEYAEAIATRAGALAGISLMFQPCVVPPKP 283
Query: 418 WRGYNRGGHFF---LPSYVMRTHGAR 440
W G GG++ P ++RTH +
Sbjct: 284 WTGITGGGYWANGRRPLALVRTHSKK 309
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 34/135 (25%), Positives = 61/135 (45%), Gaps = 10/135 (7%)
Query: 325 KPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEALKGRRY 384
+PW +++G L ++L++ + +D+ S + P H SF ++
Sbjct: 469 QPWPLPVQMELGKLLAEMLVQATQMPCSLDKPHRSS-RLVPVLYHVY-SFRNV----QQI 522
Query: 385 GVIECDPLVRKGLEKTGRHMII---PYMPMLVPPLNWRGYNRGGHFFLPSYVMRT-HGAR 440
G+++ P + LEK + +PML PPL W + G P+ +MRT GA
Sbjct: 523 GILKPHPAYVQLLEKAAEPTLTFEAVDVPMLCPPLPWTSPHSGAFLLSPTKLMRTVEGAT 582
Query: 441 QQRETIKMTPRSQLE 455
Q +E ++ P + L
Sbjct: 583 QHQELLETCPPTALH 597
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.134 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,807,147
Number of Sequences: 62578
Number of extensions: 480041
Number of successful extensions: 1091
Number of sequences better than 100.0: 128
Number of HSP's better than 100.0 without gapping: 122
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 969
Number of HSP's gapped (non-prelim): 132
length of query: 492
length of database: 14,973,337
effective HSP length: 103
effective length of query: 389
effective length of database: 8,527,803
effective search space: 3317315367
effective search space used: 3317315367
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)